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Sequence Class Reference

#include <sequence.h>

Inheritance diagram for Sequence::

List of all members.

Public Methods
	Sequence (char *newSequence, int nNr)
	Sequence (const Sequence &sequenceCopy)
virtual	~Sequence ()
char*	getPackedSequence () const
char*	getUnpackedSequence ()
virtual double	getFitness ()
virtual int	addinstance ()
virtual int	removeinstance (int nPos)
virtual int	calculate_fitness (char *pTarget)
int	operator== (const Sequence &s) const
Public Attributes
list<int>	instances
double	fitness
int	distance
int	nCopies
char*	pRNA_sequence
int	nNr
Static Public Attributes
const int	mutWay = 0
Friends
ostream&	operator<< (ostream &stream, Sequence &s)

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Detailed Description

The sequence class is the base class for the objects handled in the flowreactor, to keep a (at best compressed) sequence of RNA nucleotids, an ID, the number of copies, and a fitness and a distance value. If you plan to perform a lineage the sequence class, it is able to keep the instance-number (aka "copy" for non-programmers).

Definition at line 23 of file sequence.h.

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Constructor & Destructor Documentation

Sequence::Sequence ( char * newSequence, int nNr )

Sequence::Sequence ( const Sequence & sequenceCopy )

virtual Sequence::~Sequence ( ) [virtual]

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Member Function Documentation

virtual int Sequence::addinstance ( ) [virtual]

Reimplemented in StructSeq, MRnaSeq, and MRnaSeq.

virtual int Sequence::calculate_fitness ( char * pTarget ) [virtual]

Reimplemented in BonusSeq, StructSeq, EvalSeq, MinorSeq, CodeSeq, PkSequence, MRnaSeq, PseudoSeq, CodeSeq, and MRnaSeq.

virtual double Sequence::getFitness ( ) [virtual]

Reimplemented in BonusSeq.

char* Sequence::getPackedSequence ( ) const

Referenced by hash< const StructSeq *>::operator()(), hash< const Sequence *>::operator()(), hash< const PseudoSeq *>::operator()(), hash< const PkSequence *>::operator()(), hash< const MRnaSeq *>::operator()(), hash< const MinorSeq *>::operator()(), hash< const EvalSeq *>::operator()(), hash< const CodeSeq *>::operator()(), hash< const BonusSeq *>::operator()(), and hash< const BiEvalSeq *>::operator()().

char* Sequence::getUnpackedSequence ( )

int Sequence::operator== ( const Sequence & s ) const

virtual int Sequence::removeinstance ( int nPos ) [virtual]

Reimplemented in StructSeq, MRnaSeq, and MRnaSeq.

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Friends And Related Function Documentation

ostream& operator<< ( ostream & stream, Sequence & s ) [friend]

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Member Data Documentation

int Sequence::distance

Definition at line 31 of file sequence.h.

double Sequence::fitness

Definition at line 30 of file sequence.h.

list<int> Sequence::instances

Definition at line 29 of file sequence.h.

const int Sequence::mutWay = 0 [static]

Reimplemented in MRnaSeq. Definition at line 33 of file sequence.h.

int Sequence::nCopies

Definition at line 35 of file sequence.h.

int Sequence::nNr

Definition at line 37 of file sequence.h.

char* Sequence::pRNA_sequence

Definition at line 36 of file sequence.h.

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The documentation for this class was generated from the following file:

• sequence.h

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